Craniofacial sutures are the fibrous joints between bones, allowing growth of the skull from prenatal to postnatal development until adult size is achieved. Proper suture development is crucial because abnormal suture fusion can require major surgical intervention to restore a satisfactory head and facial appearance and to prevent secondary damage to the brain, eyes, hearing, breathing, and mastication. Craniosynostosis, the premature fusion of skull sutures, is a common birth defect, occurring in 1/2500 live births. I may present in syndromic and non-syndromic forms, and while mutations in some of the genes that account for syndromic forms are known, the underlying genetic etiology has not been identified for the majority of cases that are non- syndromic and involve a single suture. A more comprehensive understanding of suture biology and pathology can be aided by knowledge of gene expression profiles of sutures. Craniofacial sutures vary widely in form, function, and susceptibility to fusion, suggesting that gene expression profiles vary considerably among sutures and during different developmental stages. A detailed characterization of gene expression would require the extraction of specific populations of cells from the different subregions of each suture, including the non-ossifying suture mesenchyme and the flanking osteogenic bone fronts, which are often from distinct bones and may therefore have distinct gene expression patterns. Our overall goal is to generate comprehensive gene expression atlases of the major and functionally important craniofacial sutures of the mouse, which will accelerate both our understanding of human suture biology and the discovery of candidate genes whose mutation may cause craniosynostosis or other defects of craniofacial bone development. We will apply the state-of-the-art technology of laser capture microdissection to obtain tissue from different craniofacial sutures of both normal and craniosynostotic mouse models, combined with next generation sequencing of extracted RNA (RNA-Seq). In Aim 1 we will breed a mouse model of Apert syndrome craniosynostosis with the Fgfr2 S252W mutation and use laser capture microdissection to obtain cells from 11 craniofacial sutures from WT and mutant mice. A second mouse model for Saethre-Chotzen syndrome with a Twist1 heterozygous null mutation will be bred to provide a comparison for two major sutures. In Aim 2 we will extract RNA from the different sutural subregions of WT mice and perform RNA-Seq to generate a comprehensive set of gene expression atlases for normal sutures. In Aim 3 we will similarly extract RNA from the suture subregions of Apert and Saethre-Chotzen syndrome mice for RNA-Seq and generate gene expression atlases complementary to the normal gene expression atlases. These atlases will allow the rapid discovery of genes not yet known to be expressed in sutures, reveal the commonalities and differences between sutures that may suggest new hypotheses of suture formation and differentiation, with wider significance for evolutionary studies of the vertebrate skull, and provide insight into the pathology of suture fusion.